Organic farming does not allow the use of conventional mineral fertilizers and crop protection products. As a result, in our experiments we chose to grow different species of cereals and to see how cereal species affect mycotoxin accumulation. This study describes the occurrence of deoxynivalenol (DON), zearalenone (ZEA) and T-2/HT-2 toxin in a survey of spelt and common wheat and their bran as well as flour. The analysis was conducted using an enzyme-linked immunosorbent assay (ELISA) method. The concentrations of DON, ZEA and T-2/HT-2 in Triticum spelta and T. aestivum were influenced by species, cereal type and year interaction. The highest concentrations of these mycotoxins were found in spelt grain with glumes, in spelt glumes and in spring wheat. These results show significantly higher concentrations of Fusarium toxins in glumes than in dehulled grain, which indicates the possible protective effect of spelt wheat glumes. The lowest DON, ZEA and T-2/HT-2 concentrations were determined in spelt grain without glumes. The research shows that it is potentially risky to produce bran from grain in which mycotoxin concentrations are below limits by European Union Regulation No. 1881/2006, since the concentration of mycotoxins in bran can be several times higher than that in grain. As a result, although bran is a dietary product characterised by good digestive properties, it can become a harmful product that can cause unpredictable health damage.